The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and pest resistance, branch number, seed quality and yield and yield related traits, drought tolerance, and morphological traits. However, results among these studies differed due to the use of different genetic populations, markers and marker densities, and testing environments. Since two previous meta-QTL analyses were performed on fiber traits, a number of papers on QTL mapping of fiber quality, yield traits, morphological traits, and disease resistance have been published. To obtain a better insight into the genome-wide distribution of QTL and to identify consistent QTL for marker assisted breeding in cotton, an updated comparative QTL analysis is needed. In this study, a total of 1,223 QTL from 42 different QTL studies in Gossypium were surveyed and mapped using Biomercator V3 based on the Gossypium consensus map from the Cotton Marker Database. A meta-analysis was first performed using manual inference and confirmed by Biomercator V3 to identify possible QTL clusters and hotspots. QTL clusters are composed of QTL of various traits which are concentrated in a specific region on a chromosome, whereas hotspots are composed of only one trait type. QTL were not evenly distributed along the cotton genome and were concentrated in specific regions on each chromosome. QTL hotspots for fiber quality traits were found in the same regions as the clusters, indicating that clusters may also form hotspots. Putative QTL clusters were identified via meta-analysis and will be useful for breeding programs and future studies involving Gossypium QTL. The presence of QTL clusters and hotspots indicates consensus regions across cultivated tetraploid Gossypium species, environments, and populations which contain large numbers of QTL, and in some cases multiple QTL associated with the same trait termed a hotspot. This study combines two previous meta-analysis studies and adds all other currently available QTL studies, making it the most comprehensive meta-analysis study in cotton to date.

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A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton.

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

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Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Based on 1075 and 1059 QTL from intraspecific Upland and interspecific Upland × Pima populations, respectively, the identification of QTL clusters and hotspots provides a useful resource for cotton breeding.
 Mapping of quantitative trait loci (QTL) is a pre-requisite of marker-assisted selection for crop yield and quality. Recent meta-analysis of QTL in tetraploid cotton (Gossypium spp.) has identified regions of the genome with high concentrations of QTL for various traits called clusters and specific trait QTL called hotspots or meta-QTL (mQTL). However, the meta-analysis included all population types of Gossypium mixing both intraspecific G. hirsutum and interspecific G. hirsutum × G. barbadense populations. This study used 1,075 QTL from 58 publications on intraspecific G. hirsutum and 1,059 QTL from 30 publications on G. hirsutum × G. barbadense populations to perform a comprehensive comparative analysis of QTL clusters and hotspots between the two populations for yield, fiber and seed quality, and biotic and abiotic stress tolerance. QTL hotspots were further analyzed for mQTL within the hotspots using Biomercator V3 software. The ratio of QTL between the two population types was proportional yet differences in hotspot type and placement were observed between the two population types. However, on some chromosomes QTL clusters and hotspots were similar between the two populations. This shows that there are some universal QTL regions in the cultivated tetraploid cotton which remain consistent and some regions which differ between population types. This study for the first time elucidates the similarities and differences in QTL clusters and hotspots between intraspecific and interspecific populations, providing an important resource to cotton breeding programs in marker-assisted selection .

A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations.

Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome-wide association study (GWAS) of fibre quality traits. A total of 10 511 polymorphic SNPs distributed in 26 chromosomes were screened across the cotton germplasms, and forty-six significant SNPs associated with five fibre quality traits were detected. These significant SNPs were scattered over 15 chromosomes and were involved in 612 unique candidate genes, many related to polysaccharide biosynthesis, signal transduction and protein translocation. Two major haplotypes for fibre length and strength were identified on chromosomes Dt11 and At07. Furthermore, by combining GWAS and transcriptome analysis, we identified 163 and 120 fibre developmental genes related to length and strength, respectively, of which a number of novel genes and 19 promising genes were screened. These results provide new insight into the genetic basis of fibre quality in G. hirsutum and provide candidate SNPs and genes to accelerate the improvement of upland cotton.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12693

Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.

Key message
A specialized database currently containing more than 2200 QTL is established, which allows graphic presentation, visualization and submission of QTL.

Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations

Composite cross populations (CP) developed from three or more cultivars/lines are frequently used to improve agronomic and economic traits in crop cultivar development programs. Employing CP in linkage map construction and quantitative trait locus (QTL) mapping may increase the marker density of upland cotton (Gossypium hirsutum L.) genetic maps, exploit more adequate gene resources and facilitate marker-assisted selection (MAS). To construct a relatively high-density map and identify QTL associated with fiber quality traits in upland cotton, three elite upland cultivars/lines, Yumian 1, CRI 35 and 7,235, were used to obtain the segregating population, Yumian 1/CRI 35//Yumian 1/7,235. A genetic map containing 978 simple sequence repeat (SSR) loci and 69 linkage groups was constructed; the map spanned 4,184.4 cM, covering approximately 94.1% of the entire tetraploid cotton genome. A total of 63 QTL were detected, explaining 8.1–55.8% of the total phenotypic variance: 11 QTL for fiber elongation, 16 QTL for fiber length, 9 QTL for fiber micronaire reading, 10 QTL for fiber strength and 17 QTL for fiber length uniformity. The genetic map and QTL detected for fiber quality traits are promising for further breeding programs of upland cotton with improved fiber quality.

Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.)

Objectives(s) Toll-like receptors (TLRs) on platelets have been extensively studied. Both TLR2 and TLR4 have been shown to augment platelet activation and alter its function from a hemostatic regulator to an immune sentinel. However, few studies have investigated the relationship between genetic polymorphisms in TLR2, TLR4 and platelets. We investigated whether genetic polymorphisms of TLR2 and TLR4 were related to thrombocytopenia and coagulation failure in Chinese patients with sepsis. Basic Methods Adult Chinese patients with sepsis in the intensive care unit of a university medical center were monitored for up to 28 days. Thrombocytopenia and disseminated intravascular coagulation (DIC), diagnosed using Japanese Association for Acute Medicine (JAAM) criteria, were observed as the primary outcomes. Single-nucleotide polymorphisms (SNPs) in TLR2 (rs111200466, rs5743708) and TLR4 (rs11536889, rs145801336, rs11536896, rs7869402) in patients with sepsis were detected by polymerase chain reaction. The data were analyzed using chi-square and rank sum tests. Results The genotype of TLR2 (rs111200466) (Del/Del) was associated with the initial DIC. The genotype of TLR4 (rs11536889) (C/C&C/G) was associated with initial DIC, DIC onset during hospitalization and platelet counts. Furthermore, both DIC and platelet counts were associated with cytokines and chemokines, especially the IL10. Conclusion Our results demonstrate that in Chinese sepsis patients, the rs111200466 SNP in TLR2 and rs11536889 SNP in TLR4 are associated with thrombocytopenia and DIC, with potential effects on the TLR4 pathways of platelets.

https://www.dovepress.com/getfile.php?fileID=77298

Associations Among Disseminated Intravascular Coagulation, Thrombocytopenia Cytokines/Chemokines and Genetic Polymorphisms of Toll-Like Receptor 2/4 in Chinese Patients with Sepsis

The abnormal concentrations of human immunoglobulin G (hIgG) refers to many kinds of diseases. Analytical methods with the characteristics of rapid response, easy operation and high sensitivity should be designed to accurately determinate the hIgG levels in human serum. In this work, a label-free electrochemical immunosensor based on WSe2/rGO was developed to sensitively detect human immunoglobulin G. First, the flower-like transition metal dichalcogenides (TMDCs) Tungsten Diselenide (WSe2) with large effective specific surface area and porous structure was synthesized by hydrothermal synthesis. As a bio-matrix, the flower-like WSe2 efficiently increased the active sites for loading antibodies. Meanwhile, reduced graphene oxide (rGO) obtained by tannic acid reduction was used to improve the current response of the sensing interface. WSe2 was combined with rGO and the electrochemical active surface area (ECSA) of the sensing interface was enlarged to 2.1 times that of GCE. Finally, the combination of flower-like WSe2 and rGO broadened the detection range and reduced the detection limit of the sensing platform. The immunosensor exhibited a high sensitivity with a wide linear range of 0.01-1000 ng/mL and low detection limit of 4.72 pg/mL. The real sample analysis of hIgG were conducted under optimal conditions, and the spiked recovery rates were between 95.5 and 104.1%. Moreover, satisfactory results were obtained by testing the stability, specificity and reproducibility of the immunosensor. Therefore, it can be concluded that the as-proposed immunosensor has the application potential of clinical analyze of hIgG in human serum. 

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Jing Ma

Papers

Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.)

Associations Among Disseminated Intravascular Coagulation, Thrombocytopenia Cytokines/Chemokines and Genetic Polymorphisms of Toll-Like Receptor 2/4 in Chinese Patients with Sepsis

Flower-like WSe2 used as bio-matrix in ultrasensitive label-free electrochemical immunosensor for human immunoglobulin G determination